feat(cli): add client commands and home-based local runtime defaults

doc/DEVELOPING.md

@@ -21,12 +21,32 @@ This starts:
 - API server: `http://localhost:3100`
 - UI: served by the API server in dev middleware mode (same origin as API)
 
+## One-Command Local Run
+
+For a first-time local install, you can bootstrap and run in one command:
+
+```sh
+pnpm paperclip run
+```
+
+`paperclip run` does:
+
+1. auto-onboard if config is missing
+2. `paperclip doctor` with repair enabled
+3. starts the server when checks pass
+
 ## Database in Dev (Auto-Handled)
 
 For local development, leave `DATABASE_URL` unset.
 The server will automatically use embedded PostgreSQL and persist data at:
 
-- `./data/embedded-postgres`
+- `~/.paperclip/instances/default/db`
+
+Override home and instance:
+
+```sh
+PAPERCLIP_HOME=/custom/path PAPERCLIP_INSTANCE_ID=dev pnpm paperclip run
+```
 
 No Docker or external database is required for this mode.
 
@@ -49,7 +69,7 @@ Expected:
 To wipe local dev data and start fresh:
 
 ```sh
-rm -rf server/data/embedded-postgres
+rm -rf ~/.paperclip/instances/default/db
 pnpm dev
 ```
 
@@ -61,7 +81,7 @@ If you set `DATABASE_URL`, the server will use that instead of embedded PostgreS
 
 Agent env vars now support secret references. By default, secret values are stored with local encryption and only secret refs are persisted in agent config.
 
-- Default local key path: `./data/secrets/master.key`
+- Default local key path: `~/.paperclip/instances/default/secrets/master.key`
 - Override key material directly: `PAPERCLIP_SECRETS_MASTER_KEY`
 - Override key file path: `PAPERCLIP_SECRETS_MASTER_KEY_FILE`
 
@@ -85,3 +105,30 @@ Migration helper for existing inline env secrets:
 pnpm secrets:migrate-inline-env         # dry run
 pnpm secrets:migrate-inline-env --apply # apply migration
 ```
+
+## CLI Client Operations
+
+Paperclip CLI now includes client-side control-plane commands in addition to setup commands.
+
+Quick examples:
+
+```sh
+pnpm paperclip issue list --company-id <company-id>
+pnpm paperclip issue create --company-id <company-id> --title "Investigate checkout conflict"
+pnpm paperclip issue update <issue-id> --status in_progress --comment "Started triage"
+```
+
+Set defaults once with context profiles:
+
+```sh
+pnpm paperclip context set --api-base http://localhost:3100 --company-id <company-id>
+```
+
+Then run commands without repeating flags:
+
+```sh
+pnpm paperclip issue list
+pnpm paperclip dashboard get
+```
+
+See full command reference in `doc/CLI.md`.